8CC4

LasB bound to phosphonic acid based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Inhibitors of the Elastase LasB for the Treatment of Pseudomonas aeruginosa Lung Infections.

Konstantinovic, J.Kany, A.M.Alhayek, A.Abdelsamie, A.S.Sikandar, A.Voos, K.Yao, Y.Andreas, A.Shafiei, R.Loretz, B.Schonauer, E.Bals, R.Brandstetter, H.Hartmann, R.W.Ducho, C.Lehr, C.M.Beisswenger, C.Muller, R.Rox, K.Haupenthal, J.Hirsch, A.K.H.

(2023) ACS Cent Sci 9: 2205-2215

  • DOI: https://doi.org/10.1021/acscentsci.3c01102
  • Primary Citation of Related Structures:  
    8CC4

  • PubMed Abstract: 

    Infections caused by the Gram-negative pathogen Pseudomonas aeruginosa are emerging worldwide as a major threat to human health. Conventional antibiotic monotherapy suffers from rapid resistance development, underlining urgent need for novel treatment concepts. Here, we report on a nontraditional approach to combat P. aeruginosa -derived infections by targeting its main virulence factor, the elastase LasB. We discovered a new chemical class of phosphonates with an outstanding in vitro ADMET and PK profile, auspicious activity both in vitro and in vivo . We established the mode of action through a cocrystal structure of our lead compound with LasB and in several in vitro and ex vivo models. The proof of concept of a combination of our pathoblocker with levofloxacin in a murine neutropenic lung infection model and the reduction of LasB protein levels in blood as a proof of target engagement demonstrate the great potential for use as an adjunctive treatment of lung infections in humans.


  • Organizational Affiliation

    Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elastase
A, B
301Pseudomonas aeruginosaMutation(s): 0 
Gene Names: lasBPA3724
EC: 3.4.24.26
UniProt
Find proteins for P14756 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P14756 
Go to UniProtKB:  P14756
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14756
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U7F (Subject of Investigation/LOI)
Query on U7F

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
[(2~{R})-4-methyl-1-oxidanylidene-1-[[4-(trifluoromethyl)phenyl]amino]pentan-2-yl]phosphonic acid
C13 H17 F3 N O4 P
ORECNCXKBPLBGJ-LLVKDONJSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.404α = 90
b = 77.114β = 90
c = 152.205γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Database references